LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles

units           lj
atom_style      tri
atom_modify     first big map yes

read_data       data.tri.srd
Reading data file ...
  orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  1500 atoms
  1500 triangles
  read_data CPU = 0.010 seconds

# add small particles as hi density lattice

lattice         sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region          box block INF INF INF INF INF INF
lattice         sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms    2 region box
Created 91125 atoms
  using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
  create_atoms CPU = 0.005 seconds

group           big type 1
1500 atoms in group big
group           small type 2
91125 atoms in group small
set             group small mass 0.01
Setting atom values ...
  91125 settings made for mass

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 1.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0

delete_atoms    overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.8
  ghost atom cutoff = 1.8
  binsize = 0.9, bins = 19 19 19
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271

# SRD run

reset_timestep  0

velocity        small create 1.44 87287 loop geom

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes
neigh_modify    exclude molecule/intra big include big

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      tri/lj 3.5
pair_coeff      1 1 0.1 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
  create bodies CPU = 0.000 seconds
  125 rigid bodies with 1500 atoms
  1.8601881 = max distance from body owner to body atom
fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip inside ignore

fix             3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8

# diagnostics

compute         tsmall small temp/deform
compute         tbig big temp
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)

compute_modify  tbig extra/dof -4500

compute         1 big erotate/asphere
compute         2 all ke
compute         3 all pe
variable        toteng equal (c_1+c_2+c_3)/atoms

thermo          100
thermo_style    custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)

compute         10 all property/atom corner1x corner1y corner1z                 corner2x corner2y corner2z corner3x corner3y corner3z

#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump1.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]

run             1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
  SRD/big particles = 14771 1500
  big particle diameter max/min = 2.9202881 0.87320391
  SRD temperature & lamda = 1 0.2
  SRD max distance & max velocity = 0.8 40
  SRD grid counts: 17 17 17
  SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
  SRD per actual grid cell = -3.9971745
  SRD viscosity = -34.162587
  big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 19.970837 35.150443
  ave/max big velocity = 0 0
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.8
  ghost atom cutoff = 3.8
  binsize = 16.874681, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair tri/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/3d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 184.3 | 184.9 | 185.4 Mbytes
   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
         0   0              1.4502537      0             -0.15949051     0              0            
       100   0.39689465     1.1495173      0.26931663     1.0004927      1.1170389      279          
       200   0.82155086     1.0684809      0.60689485     0.81307973     1.0433122      467          
       300   1.3210872      1.0334277      1.0368935      1.0853416      0.99443391     621          
       400   1.9755695      1.0149146      1.6438403      1.7258285      0.9925525      788          
       500   3.0111365      1.0121291      2.4285289      2.5210058      0.99688885     922          
       600   4.5413799      1.014305       3.4727946      3.8290233      0.99002027     1063         
       700   6.6071849      1.0062952      4.9025772      3.9595327      0.99573591     1186         
       800   7.6256618      1.0151252      5.3662442      5.0088255      0.99640985     1371         
       900   8.1578206      1.0148959      5.7716683      6.6059298      0.96053165     1555         
      1000   10.749617      1.0282309      7.6209538      11.277602      1.0012602      1844         
Loop time of 28.4136 on 4 procs for 1000 steps with 16271 atoms

Performance: 3040.793 tau/day, 35.194 timesteps/s, 572.647 katom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.454     | 15.242     | 17.781     |  48.4 | 53.64
Neigh   | 0.093078   | 0.094516   | 0.097759   |   0.6 |  0.33
Comm    | 0.48732    | 2.9927     | 5.7363     | 107.5 | 10.53
Output  | 0.00080706 | 0.0008431  | 0.00086933 |   0.0 |  0.00
Modify  | 10.015     | 10.063     | 10.111     |   1.4 | 35.42
Other   |            | 0.02046    |            |       |  0.07

Nlocal:        4067.75 ave        4467 max        3606 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost:         2313.5 ave        2327 max        2296 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs:          24883 ave       26066 max       24145 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 99532
Ave neighs/atom = 6.1171409
Neighbor list builds = 70
Dangerous builds = 0

#undump          1
#undump          2
unfix           3

change_box      all triclinic
Changing box ...
  triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)

fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip tstat yes inside ignore

#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump2.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]

fix             3 all deform 1 xy erate 0.05 units box remap v

run             2000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 14771 1500
  big particle diameter max/min = 2.9202881 0.87320391
  SRD temperature & lamda = 1 0.2
  SRD max distance & max velocity = 0.8 40
  SRD grid counts: 13 13 13
  SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
  SRD per actual grid cell = -2.775698
  SRD viscosity = -12.180602
  big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
  # of rescaled SRD velocities = 3
  ave/max small velocity = 16.10299 40
  ave/max big velocity = 2.0311414 11.34118
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.8
  ghost atom cutoff = 3.8
  binsize = 13.499745, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair tri/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton/tri
      stencil: half/multi/3d/tri
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 148.8 | 149.5 | 150 Mbytes
   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
      1000   10.749616      1.0167438      7.6203704      5.4893075      0              0            
      1100   9.0727748      1.003438       6.1822573      8.6707036      1              1339         
      1200   7.1960998      1.0003968      4.8077632      6.7809972      1              1039         
      1300   6.2680889      1.0011134      4.3139658      8.2260362      1              861          
      1400   5.8199503      1.0024475      3.9876867      7.0322957      1              692          
      1500   5.399935       0.99757802     3.4552534      7.905565       1              577          
      1600   5.0830248      1.0023727      3.1330433      7.6897887      1              479          
      1700   4.8728937      1.0027203      3.0838267      7.606406       1              389          
      1800   4.8443541      1.0018057      3.115321       7.4547572      1              317          
      1900   5.0622362      1.0007126      2.9336473      6.514338       1              268          
      2000   5.022699       1.0030275      3.1244763      7.2999286      1              223          
      2100   4.4605894      1.0019457      2.9262733      8.3475145      1              196          
      2200   4.6544992      1.0023701      3.0140329      7.3670747      1              164          
      2300   4.1954825      1.0012089      2.5802739      7.5553707      1              142          
      2400   4.0806819      1.0000292      2.6492187      7.5648723      1              122          
      2500   3.7437189      0.99949605     2.3660722      8.2155316      1              104          
      2600   4.2333926      1.0002823      2.5704515      7.2839635      1              106          
      2700   3.7542455      1.001394       2.4146222      6.3785983      1              86           
      2800   3.4011329      0.99832028     2.141193       6.3869497      1              78           
      2900   3.4579019      1.0007319      2.1839274      6.241817       1              64           
      3000   3.6128019      1.0017345      2.2982426      5.8975992      1              55           
Loop time of 67.0194 on 4 procs for 2000 steps with 16271 atoms

Performance: 2578.358 tau/day, 29.842 timesteps/s, 485.561 katom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 36.774     | 43.583     | 50.126     |  71.5 | 65.03
Neigh   | 0.29299    | 0.3134     | 0.32399    |   2.2 |  0.47
Comm    | 0.75102    | 7.2688     | 14.075     | 174.8 | 10.85
Output  | 0.0016347  | 0.0017229  | 0.0018802  |   0.2 |  0.00
Modify  | 15.794     | 15.808     | 15.828     |   0.3 | 23.59
Other   |            | 0.04379    |            |       |  0.07

Nlocal:        4067.75 ave        4560 max        3583 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost:        2256.75 ave        2292 max        2241 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs:          23706 ave       24669 max       22450 min
Histogram: 1 0 0 0 0 0 2 0 0 1

Total # of neighbors = 94824
Ave neighs/atom = 5.8277918
Neighbor list builds = 108
Dangerous builds = 0
Total wall time: 0:01:36
